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- PDB-5ac8: S. enterica HisA with mutations D10G, dup13-15, G102A -

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Basic information

Entry
Database: PDB / ID: 5ac8
TitleS. enterica HisA with mutations D10G, dup13-15, G102A
Components1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
KeywordsISOMERASE / HISA / PROTEIN EVOLUTION / IAD MODEL / TRPF
Function / homology
Function and homology information


1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase / 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase activity / L-histidine biosynthetic process / L-tryptophan biosynthetic process / cytoplasm
Similarity search - Function
HisA, bacterial-type / HisA/PriA, bacterial-type / Histidine biosynthesis, HisA-like / Histidine biosynthesis protein / Histidine biosynthesis protein / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase / 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
Similarity search - Component
Biological speciesSalmonella enterica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.699 Å
AuthorsNewton, M. / Guo, X. / Soderholm, A. / Nasvall, J. / Andersson, D. / Patrick, W. / Selmer, M.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural and functional innovations in the real-time evolution of new ( beta alpha )8 barrel enzymes.
Authors: Newton, M.S. / Guo, X. / Soderholm, A. / Nasvall, J. / Lundstrom, P. / Andersson, D.I. / Selmer, M. / Patrick, W.M.
History
DepositionAug 12, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2Apr 26, 2017Group: Database references
Revision 1.3May 10, 2017Group: Database references
Revision 1.4Jan 10, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_name_com.name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_database_status.status_code_sf / _pdbx_poly_seq_scheme.pdb_ins_code / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_unobs_or_zero_occ_residues.PDB_ins_code / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.db_mon_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.mon_id / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_ref_seq_dif.pdbx_pdb_ins_code / _struct_ref_seq_dif.pdbx_seq_db_accession_code / _struct_ref_seq_dif.pdbx_seq_db_seq_num / _struct_ref_seq_dif.seq_num / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7324
Polymers27,4431
Non-polymers2883
Water1,964109
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.415, 86.415, 122.027
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase / Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase


Mass: 27443.373 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica (bacteria)
Gene: hisA, AIY46_13150, AL463_17045, CQW68_13095, D3346_17640, D3Q81_15095, EAW95_14430, FJR52_10950, GCH85_22590, NCTC6385_02080, ND68_15100
Plasmid: PEXP5-CT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A630AQ07, UniProt: P10372*PLUS, 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 4.6 / Details: 2.0M AMMONIUM SULFATE, 0.1M SODIUM ACETATE PH4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97634
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97634 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 30311 / % possible obs: 99.8 % / Observed criterion σ(I): 1.67 / Redundancy: 19 % / Biso Wilson estimate: 22.38 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 14.96
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 17.5 % / Rmerge(I) obs: 1.39 / Mean I/σ(I) obs: 1.67 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5AHF

5ahf


Resolution: 1.699→47.289 Å / SU ML: 0.15 / σ(F): 1.34 / Phase error: 20.63 / Stereochemistry target values: ML / Details: RESIDUES 16 -23, 180-183, 244-252 ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.2092 1529 5.1 %
Rwork0.1962 --
obs0.1969 30248 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.85 Å2
Refinement stepCycle: LAST / Resolution: 1.699→47.289 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1744 0 15 109 1868
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081823
X-RAY DIFFRACTIONf_angle_d1.1522492
X-RAY DIFFRACTIONf_dihedral_angle_d13.254667
X-RAY DIFFRACTIONf_chiral_restr0.049301
X-RAY DIFFRACTIONf_plane_restr0.005319
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6994-1.75420.31711200.28392508X-RAY DIFFRACTION98
1.7542-1.81690.26781580.26452544X-RAY DIFFRACTION100
1.8169-1.88970.26411310.24332572X-RAY DIFFRACTION100
1.8897-1.97570.25451360.21862572X-RAY DIFFRACTION100
1.9757-2.07980.24291400.21242566X-RAY DIFFRACTION100
2.0798-2.21010.23291200.21022611X-RAY DIFFRACTION100
2.2101-2.38080.2321370.19922591X-RAY DIFFRACTION100
2.3808-2.62040.21191440.20192614X-RAY DIFFRACTION100
2.6204-2.99950.20281540.20472613X-RAY DIFFRACTION100
2.9995-3.77880.2161410.17292674X-RAY DIFFRACTION100
3.7788-47.30730.15941480.17342854X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.2622-1.7182-3.17382.92680.78494.3062-0.32690.0141-0.15060.0330.1114-0.51560.39280.38910.32120.22720.0041-0.00230.21180.01190.2813-7.0448-32.1172-8.2457
21.61251.46032.48067.62140.84064.13090.3006-0.79210.08681.02670.27890.41050.57280.1473-0.63190.55210.00790.10420.73820.02921.217-4.1482-42.3281-5.4265
33.2615-0.43952.68796.4189-2.07323.2575-0.21230.2027-1.2935-0.27240.1564-0.89470.24270.45450.12680.3299-0.05150.0770.3506-0.02010.4669-8.5702-36.9394-15.7063
42.01731.73670.02643.16690.35512.3666-0.04890.0822-0.2665-0.12340.0898-0.42760.13210.3142-0.03290.22830.00780.00410.2116-0.01290.2208-4.3714-25.6243-11.5614
51.6767-0.84941.65810.9435-0.13633.1535-0.12120.02150.15280.02220.0636-0.0737-0.09340.04990.06930.2165-0.0095-0.01440.19670.01340.21370.2026-15.471-2.3856
66.2292-1.46090.13695.50440.24752.6223-0.315-0.314-0.32410.47290.2975-0.10910.2548-0.00110.01480.28750.055-0.01710.2579-0.02130.23020.9-25.594214.8753
74.3494-0.28980.82533.79310.37413.95340.0936-0.2061-0.15330.25020.06730.23180.3765-0.1692-0.23460.22110.0062-0.02370.19580.00370.2026-6.0841-20.15377.9386
81.24772.0549-0.10235.5147-0.02970.01980.6003-0.1799-1.01170.4787-0.622-0.34761.1620.1009-0.15680.7090.1012-0.08250.50130.01840.5654-14.5289-30.513712.7057
91.09271.33391.45074.14323.64273.23650.1251-0.2635-0.07350.4846-0.07630.05120.4213-0.2624-0.01990.2748-0.0379-0.00860.24590.01250.199-16.2669-27.69674.5797
105.3510.06110.32952.2083.58667.7790.0696-0.37690.37920.7522-0.1540.82570.0654-0.69280.09890.2872-0.05470.02430.2617-0.03960.297-25.9085-28.8508-0.8412
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:14)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 15:26)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 27:33)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 34:86)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 87:130)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 131:156)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 157:177)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 178:186)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 187:236)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 237:247)

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